Perl modules for UPGMA algorithm

Heikki Lehvaslaiho heikki at ebi.ac.uk
Fri Apr 6 03:20:11 EST 2001


Santi Garcia-Vallve wrote:
> 
> Dear Colleagues,
> 
> I want to create a web server to compare the codon usage of a group of
> genes. The method that our research group has used succesfully consists in
> calculating the codon usage of each gene, make a distance (derived from a
> correlation coeficient) matrix for every pairwise comparisons and
> constructing a dendogram using the UPGMA algorithm. Now, we use our own
> FORTRAN programs and the program growtree from GCG. To do the same in a web
> server I will rewritte our programs in Perl and create a CGI, but I need
> some help with the UPGMA algorithm. Does anybody know where I can find a
> PERL routine for the UPGMA algorithm? I have ckecked the bioperl modules
> but it seems that there are not modules about constructing phylogenetic
> trees.
> 
> Do you think it will be useful a web server like this?

Dear Santi,

I can not say if there are enough people to use the web service, but
if were to go through the trouble of putting the code in BioPerl
classes am sure it would be widely used. You are cordially invited to
join the BioPerl developers! You know were to find us.

Someone at the BioPerl list might even have the UPGMA already
implemented...

	-Heikki


> Thanks
> 
> ******************************************
> * Dr Santi Garcia-Vallve                 *
> * Bioinformatics Group                   *
> * Biochemistry and Biotechnology Dept.   *
> * Rovira i Virgili University            *
> * Pl. Imperial Tarraco, 1                *
> * 43005  Tarragona                       *
> * Spain                                  *
> *                                        *
> * telef: 34 977 559565                   *
> * fax: 34 977 558232                     *
> * email: vallve at quimica.urv.es           *
> *                                        *
> *  In the end                            *
> *   We will conserve only what we love,  *
> *   We will love only what we know,      *
> *   We will know only what we are taught *
> *                                        *
> *    -Baba Dioum, Senegalese Biologist   *
> *                                        *
> ********                       ***********
> 
> ---

-- 
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho          heikki at ebi.ac.uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
  _/  _/  _/  Cambs. CB10 1SD, United Kingdom
     _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
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